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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...a small effect on the trait, but due to the large number of 39 causal variants, they contribute substantially to trait variation. 40 Two main experimental designs are used to dissect genetic variation in complex traits. Genetic 41 mapping by linkage analysis involves crossing genetically different...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...projection of z-stack images, and others are single slice images. Quantifications were performed using Fiji (Supplemental Methods; Schindelin et al. 2012).Wild-type and catalytically inactive mutant hsKDM4D expression vector cloningTotal RNA from 2 d-post-fertilization medaka embryos and HEK293 were reverse...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...Kohei Hagiwara, Andrew Thrasher, Nadezhda V. Terekhanova, and Jinghui Zhang Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA Allele-specific expression (ASE) of somatic mutations can be caused by cis-activation of the mutant allele...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...-8585, Aichi, Japan ↵5 These authors contributed equally to this work. Corresponding authors: naruse@nibb.ac.jp, qtu@genetics.ac.cnAbstractMedaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...and species (Lieberman-Aiden et al. 2009; Dixon et al. 2012; Sexton et al. 2012; Kaaij et al. 2018).View larger version: In this window In a new window Figure 1. 3D structure of medaka fibroblast cells and CTCF positioning throughout medaka development. (A) Hi-C contact map of medaka fibroblast cells...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...), NPC lines, and developmental timepoints, to generate a list of putative enhancer regions to investigate using the phNPC model. Whereas other enhancer mapping tools such as massively parallel reporter assays (MPRAs) have been used to identify putative enhancer regions in primary human cortical cells...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...are indeed proximal in physical space and vice versa. A CTG distance matrix is constructed based on the similarity of the diffusion property between genomic loci in the Hi-C contact map. Except for self-distance, the calculation of CTG distance (L1 distance between rows of transition probability matrix...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...lymphoblastoid cell line (EBV-LCL). The DNA was used as input for the preparation of ultra long-read ONT sequencing libraries. Sequencing was performed using an adaptive sampling strategy to enrich for reads mapping to the IGH locus. (B) Read depth from the four donors on a custom IGH reference. (C) Outline...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
.... The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...were functionally annotated by mapping them to in-house profiles of the Clusters of Orthologous Genes (COG) database (2020 release) (Galperin et al. 2021) with HMMER v3.1b2 (e-value < 0.001; http://hmmer.org). The 26 major prokaryotic functional categories defined in the COG database were assigned...
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